This project's focus is on two infectious diseases that continue to have tremendous impact on global health. Human Immunodeficiency Virus (HIV) is pandemic and Hepatitis B Virus (HBV) infection and HBV-associated hepatocellular carcinoma (HCC) is prevalent in East Asia, globally affecting millions of people and having no cure. The objective of this project is to identify host factors that contribute to the occurrence and development of these, and potentially other, infectious diseases. We aim to identify host genetic factors that affect host innate restriction or susceptibility in acquisition, replication, and pathogenesis of viral pathogens, and carcinogenesis, the mechanisms of which are not fully understood. The identification of host proteins involved in viral replication, in innate or acquired immunity, or in carcinogenesis pathways will provide critical insights for the rational development of antiviral drugs and effective vaccines. Our strategy is to search for genetic variants that differentially affect rates of infection, or the course of pathogenesis, and which thereby identify the variant-containing gene as conferring restriction or susceptibility to infection or progression. We are using both targeted gene and genome wide association study (GWAS) approaches, including Illumina and Affymetrix chip technologies, to discover genes associated with HIV-1, HBV infection and HBV-associated liver cancer. Accomplishments 1) Human APOBEC3 cytidine deaminases are a family of intrinsic retroviral resistance factors that edit viral RNA, leading to nascent DNA hypermutation. However, HIV-1 viral infectivity factor (Vif) binds to APOBEC3 proteins and targets it for degradation via the ubiquitination-proteosomal pathway; therefore HIV is resistant to APOBEC3 restriction. APOBEC3F (A3F) anti-HIV-1 activity is partially resistant to Vif degradation unlike APOBEC3G. In vitro studies have shown that A3F edits the HIV-1 genome similarly to APOBEC3G, albeit with different target sequences and with weaker anti-HIV activity. To assess the in vivo effect of A3F gene on host susceptibility to HIV- acquisition and disease progression, we performed a genetic association study in six well-characterized HIV-1 natural cohorts. A common six-SNP haplotype of A3F tagged by a codon-changing SNP (p. I231V) was associated with significantly lower set-point viral load and slower rate of progression to AIDS (RH = 0.71, 95% CI: 0.56, 0.91). The slower rate of progression to AIDS was mainly afforded by delayed development of pneumocystis pneumonia (PCP) (RH= 0.53, 95% CI: 0.37-0.76). A validation study in the International Collaboration for the Genomics of HIV (ICGH) showed a consistent association with lower set-point viral load. The HIV-1 Vif protein, which shares sequence homology and structurally mimics the A3F region containing p.I231V, may have evolved to adapt to the host p. I231V isoforms, suggesting that the A3F I231V change may modify A3F-vif interaction. Our results provide genetic epidemiological evidence that A3F modulates HIV-1/AIDS disease progression. The results have been formalized for publication and submitted. 2) ZNRD1 was identified as a host protein required for the completion of the HIV lifecycle in a genome-wide screen using small interfering RNA gene silencing. Subsequently, a genome-wide association study (GWAS) of host determinants for HIV-1 disease identified an association of single nucleotide polymorphisms (SNPs) in the ZNRD1 region with CD4 T-cell depletion. To address the effects of SNPs in the ZNRD1 region on human immunodeficiency virus type 1 (HIV-1) infection and progression to clinical outcomes, we determined the association of ZNDR1 variants in 5 US-based HIV-1 longitudinal cohorts (n = 1865). SNP function was evaluated by electrophoretic mobility shift assay and promoter luciferase assay. A haplotype in the ZNRD1 gene showed significant association with a 35% decreased risk of HIV-1 acquisition (OR = 0.65,95% CI, .47-.89), independent of HLA-C rs9264942, in European Americans. The SNP rs3132130 tagging this haplotype, located in the ZNRD1 5' upstream region, caused a loss of nuclear factor binding and decrease in ZNRD1 promoter activity. ZNRD1 variants also affected HIV-1 disease progression in European- and African-American cohorts.We concluded that that ZNRD1 polymorphism may confer host resistance to HIV-1 acquisition. This study was published in the Journal of Infectious Diseases. 3) The APOL1 gene, encoding apolipoprotein L1, confers resistance to Trypansoma brucei, the cause of African trypanosomiasis. APOL1 G1 (S342G:I384M) and G2 (6 bp deletion) alleles restore resistance to trypanosomes causing acute human trypanosomiasis and are found only in individuals with recent African ancestry. APOL1 variant alleles are recessively associated with increased risk for HIV-associated nephropathy (OR 27-89); approximately12-14% of the AA population carry high-risk genotypes. Since apolipoproteins have antiviral properties and are up-regulated by interferons, we tested APOL1 variants for association with HIV. In vitro studies by others demonstrated that APOL1 inhibits HIV-1 replication by several mechanisms; the in vivo role of APOL1 variants on HIV-1 infection, progression, and disease outcomes has not been investigated. We determined APOL1 genotypes for AA enrolled in two HIV cohorts in a collaborative study with investigators at Johns Hopkins University. In an African American cohort (n = 749), 7.7% of AA HIV+ carried high-risk genotypes compared to 12% of at-risk HIV- individuals (OR 0.60, 95% CI: 0.33-1.08; P = 0.09). High-risk genotypes were associated with a 71% decrease in the odds of opportunistic infection (OI) (OR 0.29, 95% CI: 0.09, 0.97; P = 0.04). Carriage of high-risk genotypes was associated with a non-significant decrease in the odds of prevalent OI at enrollment (OR 0.66, 95% CI: 0.40, 1.11; P = 0.11), which was mainly driven by a protective association with fungal infection (OR 0.54, 95% CI: 0.32, 0.93; P = 0.02). In summary, APOL1 G1/G2 variants were not associated with viral load or AIDS progression, but APOL1 association with resistance to HIV acquisition and opportunistic infections cannot be excluded. These results, requiring further validation, suggest a potential anti-pathogen role for APOL1 protein. 4) APOL1 variants are associated with HIV-associated nephropathy and FSGS in African Americans. The prevalence of these variants in African populations with CKD in HIV-1 infection has not been investigated. We determined the role of APOL1 variants in 120 patients with HIV-associated nephropathy and CKD and 108 controls from a South-African black population. Patients with CKD were selected on the basis of histology. Genotypes were successfully determined for APOL1 G1 and G2 variants and 42 single nucleotide polymorphisms, including 18 ancestry informative markers, for 116 patients with CKD (96.7%; 38 patients with HIV-associated nephropathy, 39 patients with HIV-positive CKD, and 39 patients with HIV-negative CKD), and 108 controls (100%). Overall, 79% of patients with HIV-associated nephropathy and 2% of population controls carried two risk alleles. In a recessive model, individuals carrying any combination of two APOL1 risk alleles had 89-fold higher odds (95% confidence interval, 18 to 912; P0.001) of developing HIV-associated nephropathy compared with HIV-positive controls. APOL1 risk alleles were not significantly associated with other forms of CKD. These results indicate HIV-positive, antiretroviral therapy-naive South-African blacks with two APOL1 risk alleles are at very high risk for developing HIV-associated nephropathy. Further studies are required to determine the effect of APOL1 risk variants on kidney diseases in other regions of sub-Saharan Africa.